title: Loss of TBX3 enhances pancreatic progenitor generation from human pluripotent stem cells [Pancreas RNA-seq]

summary: Tbx3 regulates liver development in the mouse, but it's role in human liver development is unclear. We generated TBX3 knockout pluripotent stem cell lines and found that liver differentiation is also impaired in humans. Interestingly we noted expression of pancreas-specific genes during the liver differentiation in the TBX3 knockout line.To further investigate this phenomenon, we performed RNA-seq on cells from two stages of the pancreatic differentation. These studies demonstrated that the loss of TBX3 enhances pancreatic-gene signature, implicating TBX3 as a regulator of fate decisions.

overall_design: Wildtype and TBX3 knockout plurpotent stem cells lines were differentiated to pancreatic progenitors. mRNA gene expression profiles were examined at two stages of pancreatic differentiation: Day 6 (gut tube stage) and Day 8 (pancreatic progenitor 1 stage). Three biological replicates were analyzed for each stage (two genotypes, two stages per genotype)


title: Loss of TBX3 enhances pancreatic progenitor generation from human pluripotent stem cells [Hepatoblast RNA-seq]

status: Public on Oct 14 2021

city: Philadelphia

first: Paul

last: Gadue

state: PA

address: 3501 Civic Center Blvd Room 5012

country: USA

institute: Children's Hospital of Philadelphia

type: Expression profiling by high throughput sequencing

summary: Tbx3 regulates liver development in the mouse, but it's role in human liver development is unclear. We generated TBX3 knockout pluripotent stem cell lines and found that liver differentiation is also impaired in humans. Interestingly we noted expression of pancreas-specific genes during the liver differentiation in the TBX3 knockout line. To further investigate this phenomenon, we performed RNA-seq on cells at the hepatoblast stage of the liver differentiation. These studies demonstrated that the loss of TBX3 enhances pancreatic-gene signature, implicating TBX3 as a regulator of fate decisions.

overall_design: Wildtype and TBX3 knockout plurpotent stem cells lines were differentiated to hepatocytes. mRNA gene expression profiles were examined at the heptoblast stage of the liver differentiation (Day 12 Hepatoblast stage). Three biological replicates were analyzed for each stage (two genotypes, one stage per genotype)

first: Somdutta

last: Mukherjee

first: Deborah

last: French


title: XRN2

status: Public on Oct 15 2021

city: Oklahoma City

first: Julio

middle: Cesar

last: Morales

state: OK

department: Department of Neurosurgery

institute: University of Oklahoma Health Science Center

summary: Analyzing XRN2-mediated transcriptome changes of glioblastoma multiforme cell lines

overall_design: LN229 and U251 glioblastoma multiforme established cell lines were either mock, sicontrol, or siXRN2 transfected.  Total RNA was harvested and MiSeq for transcriptome changes.

middle: C

first: Tuyen

middle: T

last: Dang


title: Perivascular niche cells sense thrombocytopenia and activate platelet-biased HSCs in an IL-1 dependent manner

city: London

first: Tiago

last: Cunha Luis

address: South Kensington, Sir. Alexander Fleming Building

department: Department of Life Sciences

country: United Kingdom

institute: Imperial College London

summary: RNA sequencing analysis of stromal cells, haematopoietic stem cells and megakaryocytes from mice in homeostasis and after platelet depletion

overall_design: Cells were isolated from mice 1 day post treatment with anti-CD42b or IgG control antibodies. 3 biological replicates (individual mice) for each of the 10 populations investigated. Each samples was prepared from 100 cells.

last: Luis

first: Nikolas

last: Barkas

first: Alice

last: Giustacchini

first: Tiphaine

last: Bouriez-Jones

first: Sten

middle: E

last: Jacobsen


title: Anabolic resistance of skeletal muscle in cancer cachexia is caused by impaired IGF1 expression to mechanical loading

city: Hiroshima

first: Mitsunori

last: Miyazaki

state: Hiroshima

address: 1-2-3 Kasumi, Minami-Ku

department: Graduate School of Biomedical and Health Sciences

country: Japan

institute: Hiroshima University

summary: Cachexia is a systemic metabolic syndrome characterized by loss of fat and skeletal muscle mass in chronic wasting diseases such as cancer. The regulation of cellular protein synthesis in response to workload in skeletal muscle is generally blunted in cancer cachexia; however, the precise molecular regulation is largely unknown. In this study, to examine the molecular mechanism of skeletal muscle protein metabolism in cancer cachexia, we analyzed comprehensive gene expression in skeletal muscle using microarrays. CD2F1 mice (male, 7 weeks old) were subcutaneously transplanted (1*10^6 cells per mouse) with a mouse colon cancer-derived cell line (C26) as a model of cancer cachexia. Functional overload of the plantaris muscle by synergist ablation was performed at the 2nd week, and the plantaris muscle was sampled at the 4th week of cancer transplantation. The hypertrophy of skeletal muscle (increased skeletal muscle weight/protein synthesis efficiency and activation of mTOR signaling) associated with compensatory overload was significantly suppressed with the cancer cachexia. Gene expression profiling and pathway analysis by microarray showed that resistance to muscle protein synthesis associated with cancer cachexia was induced by downregulation of insulin-like growth factor-1. These observations show that cancer cachexia induces resistance to muscle protein synthesis, which could be a potential factor inhibiting the adaptation of skeletal muscle growth to physical exercise.

overall_design: Colon 26 (C26) carcinoma tumor-bearing CD2F1 mice were employed as the model for the study of cancer cachexia. The C26 carcinoma (RCB2657) was provided by RIKEN BRC through the National Bio-Resource Project of MEXT, Japan. All cell culture experiments were performed in a humidified environment at 37 °C in a 5% CO2 atmosphere. The C26 cells were grown in RPMI-1640 medium (FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) supplemented with 10% FBS and penicillin–streptomycin. After trypsinization and neutralization, 1 × 10^6 C26 cells per individual were suspended with 100 μL of PBS and subcutaneously implanted into the flank region of the abdominal wall unilaterally using a 26G syringe as previously described. The control group was injected with an equal amount of PBS.


title: ESRRB facilitates the conversion of Trophoblast-like Stem Cells from induced pluripotent stem cells by directly regulating KRT8 and CDX2

city: Yangling

first: Shuai

last: YU

address: No.22 Xinong Road,

country: China

institute: Northwest A&F University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: ESRRB facilitates the conversion of Trophoblast-like Stem Cells from induced pluripotent stem cells by directly regulating KRT8 and CDX2 [RNA-seq]

summary: Studies on porcine induced pluripotent stem cells (piPSCs) served as a great reference for human clinical research. However, the pluripotency genes network of piPSCs, especially the core transcription factor ESRRB, was currently poor understand. Here, we constructed an overexpressing ESRRB piPSC line (ESRRB piPSCs) in which ESRRB expression was efficiently enhanced. It was found that ESRRB piPSCs showed scattered and flat colonies, moreover, the ESRRB piPSCs showed higher chimeric capacity into trophectoderm than that of CON piPSCs. We also found that ESRRB could directly regulate the expressions of the trophoblast stem cells (TSCs) markers, such as KRT8, KRT18 and CDX2, through binding in their promoter regions. Functional analysis of the mutant domains of ESRRB proved. that the zinc finger domain was indispensable for ESRRB to regulate TSCs markers. Moreover, the regulated process needed the participation of OCT4. Accordingly, ESRRB cooperating with OCT4 promoted TSCs markers to facilitate the conversion from the pluripotent state to trophoblastic-like state. Our results revealed the unique and crucial role of ESRRB in the determination of piPSCs fate and provided opportunities for studying the barriers underlying embryonic and extra-embryonic lineage segregation.

overall_design: RNA-seq in CON and ESRRB-piPSCs

first: Yu

last: Shuai

first: Hua

last: Jinlian


title: Human cytomegalovirus expands a T cell population with loss of BCL11B expression and gain of NK cell identity

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: CD8+ T cells, critical mediators of adaptive immunity, may also exhibit innate-like properties, such as surface expression of NKG2C, an activating receptor typically associated with natural killer (NK) cells. We demonstrate that, similar to NK cells, NKG2C+TCRαβ+CD8+ T cells are associated with prior HCMV exposure. In addition to expressing several NK cell markers (CD56, KIR), NKG2C+CD8+ T cells are oligoclonal and do not upregulate PD1 despite chronic activation. Furthermore, NKG2C+CD8+ T cells from some individuals exhibit high effector function against leukemia cells and HCMV-infected fibroblasts, dictated by NKG2C and TCR specificity. Importantly, we observe that co-triggering of CD3 and NKG2C results in increased degranulation and IFN-γ production by NKG2C+CD8+ T cells in an additive fashion. Transcriptomic analysis reveals that the transcription factor BCL11B, a regulator of T cell developmental fate, is significantly down-modulated in NKG2C+CD8+ T cells when compared to conventional NKG2C-CD8+ T cells. BCL11B deletion in conventional CD8 T cells results in the emergence of a CD56+CD94+DAP12+NKG2C+CD45RA+CCR7-PD1-/low T cell population with activity against HLA-E+ targets. Given their intrinsic capacity to recognize diseased cells coupled with lack of PD-1 upregulation despite chronic stimulation, NKG2C+CD8+ T cells represent a novel lymphocyte population that straddles the boundary between innate and adaptive immunity, presenting an attractive alternative for cellular therapy, including CAR T-based therapies.

overall_design: RNA-seq was performed on CD8 T cells and NK cells harvested from PBMCs.

middle: M

first: Katharine

last: Hsu


title: Metabolic remodeling during early murine early embryo development

city: Hangzhou

first: Jing

last: Zhao

address: Yuhang Road 866

institute: Zhejiang University

summary: During early mammalian embryogenesis, dynamic changes in cell growth and proliferation are tightly linked to the underlying genetic and metabolic regulation. However, our understanding of metabolic reprogramming and its impact on epigenetic regulation in early embryo development remains elusive. We reconstruct their metabolic landscapes from the 2-cell and blastocyst stages, as well as their transition from totipotency to pluripotency. While 2-cell embryos favor methionine, polyamine and glutathione metabolism and stay in a more reductive state, blastocyst embryos have higher mitochondrial metabolites related to the tricarboxylic acid cycle, and present a more oxidative state. Moreover, we identify a reciprocal relationship between α-ketoglutarate (α-KG) and the competitive inhibitor of α-KG-dependent dioxygenases, L-2-hydroxyglutarate (2-HG), where 2-cell embryos inherited from oocytes and 1-cell zygotes display higher L-2-HG, whereas blastocysts show higher α-KG.Supplementing 2-HG or knocking down L2hgdh, a gene encoding the 2-HG consuming enzyme L-2-hydroxyglutarate dehydrogenase  impeded erasure of global histone methylation markers . Together, our data demonstrate dynamic and interconnected metabolic, transcriptional and epigenetic network remodeling during murine early embryo development.

overall_design: We have finished the RNA-seq to investigate the effect of 2-HG and α-KG on early mouse embryo from 2PN to blastocyst. The blastocyst was used to perform the high-throughput analysis.

last: Yu

first: Jin

last: Zhang


title: Cardiomyocyte TLR4 regulates autophagy through TRAF6-mediated TFEB ubiquitination in sepsis-associated cardiac dysfunction

city: Beijing

first: Xiaoping

last: Wang

state: Beijing

address: No. 5, Dongdan Santiao, Dongcheng District, Beijing

institute: Peking Union Medical College

summary: Sepsis-associated cardiac dysfunction (SACD) is the predominant cause of death in sepsis patients with undefined mechanism of inflammation-autophagy interaction to date. Herein, time-course analysis of cardiac autophagy was conducted in a mouse model of SCAD. An in vitro model established by Lipopolysaccharide-induced macrophage conditioned media stimulation on cardiomyocytes was further investigated for molecular insights. We show cardiomyocyte Toll-like receptor 4 (cTLR4) serves as a central receptor mediating the crosstalk between cardiomyocyte and macrophage, and activation of cTLR4 intensifies the impairment of autophagic flux in cardiomyocytes. Mechanistically, the activation of cTLR4 inactivates TFEB, which largely depends on the E3 ligase activity of TRAF6. Moreover, computational simulation combined with experimental validation revealed the unique local electrostatic interactions between TRAF6 and TFEB. Collectively, our results highlight a previously undescribed role of cTLR4-TRAF6-TFEB signaling in modulating cardiac injury and identify the TRAF6-binding motif in TFEB as an attractive target for SACD therapy.

overall_design: Cardiac mRNA profiles of saline-injected control mice and LPS-stressed 24 h mice

first: Sheng

last: Gao

first: Yong

first: Wei


title: Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

type: Non-coding RNA profiling by high throughput sequencing

summary: In eukaryotes, small RNAs (sRNAs) play critical roles in multiple biological processes. Dicer endonucleases are central to sRNA biogenesis. In plants, DICER-LIKE PROTEIN 3 (DCL3) produces 24-nt small interfering RNAs (siRNAs) that determine the specificity of the RNA-directed DNA methylation (RdDM) pathway. Here, we determined structure of a DCL3-pre-siRNA complex in an active dicing-competent state. The 5′-phosphorylated-A1 of the guide strand and the 1-nt 3′-overhang of the complementary strand are specifically recognized by a positively charged pocket and an aromatic cap, respectively. The 24-nt siRNA length dependence relies on the separation between the 5′-phosphorylated-end of the guide RNA and dual cleavage sites formed by the paired RNaseIII domains. These structural studies, complemented by functional data, reveal insights into the dicing principle for Dicers in general.

overall_design: This dataset includes small RNA-seq to understand the in vivo molecular mechanism of Arabidopsis DCL3 protein.

first: Yan

last: Xue


city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: To study the effect of siRNA-mediated E2F1 and E2F2 silencing in growth-stimulated prostate cancer cells.

overall_design: Human LNCaP prostate cancer cells were transfected with siRNA SmartPools targeting E2F1, or E2F2 or a non-targeting siRNA SmartPool.  Forty-two hours after transfection, cells were treated with synthetic androgen R1881 (0.1nM) or vehicle.  Three biological replicates were generated per treatment group.  Forty-eight hours later, total RNA was isolated and processed for RNA-Seq analysis.

first: Salma

last: Ben-Salem

first: Qiang

last: Hu

first: Song

last: Liu

first: Hannelore

last: Heemers


title: Global gene expression profile of anti-CD3/CD28 or PMA/ionomycin stimulated CD4+ T cell, wild type and Mapk1-KO CD4+ T cells, and empty vector and sh-Zfp831 infected CD4+ T cells

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: Several factors promote Tfh cell differentiation. In order to understand how they promotes the expression of Tfh signature genes, we conducted transcriptional analysis.

overall_design: Naive CD4+ T cells were sorted from wild type or Mapk1-KO mice and activated under various conditions. Under specified condition, empty vector or pMKO.1-sh-Zfp831 were viral transfected into cells. Three days later, the total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions. RNA-seq library was constructed and sequenced with BGI500 platform by BGI Genomics and successfully mapped to mouse genome. Reads counts were normalized based on RPKM/FPKM, fold changes were calculated for all possible comparisons.

first: Siyuan

last: Wan

first: Xiaohong


title: Beta-catenin in cholangiocytes regulates immune environment and wound healing after hepatobiliary injury

city: Pittsburgh

first: Shuchang

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Identify differentially expressed genes in small mice cholangiocyte cell line (SMCC) when CTNNB1 is activated or silenced.

overall_design: Totally 12 samples were included: 3 for CTNNB1 activation (SMCC-S45Y), 3 for CTNNB1 activation control (SMCC-eGFP), 3 for CTNNB1 silencing (SMCC-sibcat), 3 for CTNNB1 silencing control (SMCC-siCTL)

first: Shikai

first: Jacquelyn

middle: O

last: Russell

first: Silvia

first: Ravi

last: Rai

first: Karis

last: Kosar

first: Ed

last: Hurley

first: Minakshi

last: Poddar

first: Sucha

last: Singh

first: Amaia

last: Lujambio

first: Aatur

last: Singhi

first: Aaron

last: Bell

first: Reben

last: Raeman

first: Kari

last: Nejak-Bowen

first: Sungjin

last: Ko

first: Satdarshan

middle: P

last: Monga


title: ESRRB facilitates the conversion of Trophoblast-like Stem Cells from induced pluripotent stem cells by directly regulating KRT8 and CDX2 [ChIP-seq]

first: Shuai

last: YU

overall_design: CHIP-seq of Flag in ESRRB-piPSCs

first: Yu

last: Shuai

first: Hua

last: Jinlian


title: Essential role of ALKBH5-mediated RNA demethylation modification in bile acid-induced gastric intestinal metaplasia

city: Shanghai

first: Ben

last: Yue

address: 160 Pujian Road

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

type: Methylation profiling by high throughput sequencing

summary: Reflux of bile acids and subsequent caudal-related homeobox 2 (CDX2) activation contribute to gastric intestinal metaplasia (IM), which is a precursor of gastric cancer. However, the underlying mechanism by which bile acids cause this is not entirely clear. Here we demonstrated that alkylation repair homolog protein 5 (ALKBH5), which is a major RNA N6-adenosine demethylase, was required for bile acid-induced gastric IM. Mechanistically, we revealed the N6-methyladenosine (m6A) modification profile in gastric IM for the first time and identified ZNF333 as a bona fide m6A target of ALKBH5. ALKBH5 was shown to demethylate ZNF333 mRNA, leading to enhanced ZNF333 expression by abolishing m6A-YTHDF2-dependent mRNA degradation. In addition, ALKBH5 activated CDX2 and downstream intestinal markers by targeting the ZNF333/CYLD axis and activating NF-κB signaling. Reciprocally, p65, which is the key transcription factor of the canonical NF-κB pathway, enhanced the transcription activity of ALKBH5 in the nucleus, thus forming a positive feed-forward circuit. In addition, ALKBH5 levels were positively correlated with ZNF333 and CDX2 in IM tissues, indicating a significant clinical relevance. Collectively, our findings suggest an m6A modification-associated positive feed-forward loop between ALKBH5 and NF-κB signaling is involved in the generation of the IM phenotype from gastric epithelial cells. Targeting the ALKBH5/ZNF333/CYLD/CDX2 axis might be a useful therapeutic strategy for gastric IM in patients with bile regurgitation.

overall_design: We compared the RNA m6A sites in CDCA treated GES-1 cells and control, and input was analyzed for gene expression level.


title: Revealing pathways associated with feed efficiency and meat quality traits in slow-growing chicken

city: Nakhonratchasima

first: Chotima

last: Poompramun

state: Nakhon Ratchasima

address: School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology

country: Thailand

institute: Suranaree University of Technoogy

summary: Improvement of feed efficiency would increase profitability of the poultry industries by decreasing the amount of feed required for production. Korat (KR) chicken is a new alternative meat-type chicken breed which its meat is recognized for its high protein, low fat and low purine content, whereas its low feed efficiency leads to high cost of production. Deeper understanding on how feed efficiency influences meat quality is poorly elucidated. To fulfill deeper understand molecular key that point the variation in feed efficiency and meat quality, the aim of this study was to investigate molecular pathways and genes involved in feed efficiency and meat quality in thigh of slow-growing KR chicken. A total of 75 males KR chicken were reared in individual cage until 10 weeks of age. Individual feed intake and body weight were collected weekly to calculate Feed Conversion Ratio (FCR) and Residual Feed Intake (RFI).  Meat quality parameters were measured in thigh muscles such as ultimate pH (pHu), water-holding capacity (WHC), drip loss (DL), nucleotides content and several biomolecules (amide, …). Base on extreme values of FCR at 10 weeks of ages, 12 birds from the high FCR group (HFCR) and 9 birds from the low FCR group (LFCR) were selected for investigating their transcriptome using an 8×60K Agilent chicken microarray. In addition, a weighted gene coexpression network analysis was performed to detect the relationship between modules of co-expressed genes and feed efficiency, meat quality in thigh muscle. The result in this study indicated that selection on feed efficiency (FCR, RFI) would affect flavor precursor, lipid and protein content in thigh muscle. Based on WGCNA and functional enrichment analysis, results suggested that the key molecular pathways relate to FCR, RFI and meat quality (WHC, DL, IMP, AMP and inosine) in thigh muscle were the pathways of regulation of biological process, biological regulation and regulation of metabolic. Moreover, we revealed four genes there are assembly competence domain (ACD) gene, baculoviral IAP repeat containing 5 (BIRC5) gene, cytochrome c oxidase assembly factor 3 (COA3) gene and myosin light chain 9 (MYL9) gene that might be biomarker gene in feed efficiency and meat quality in thigh muscle. The hypothesis of the current study was alteration feed efficiency in slow-growing chicken will impact meat quality especially in term of texture and flavor.

overall_design: Gene expression was measured in thigh muscles from two groups: high FCR (HFCR, n=12) and low FCR (LFCR, n=9), at 10 weeks of age.

first: Christelle

last: Hennequet-Antier

first: Kanjana

last: Thumanu

first: Wittawat

last: Molee

first: Amonrat

first: Elisabeth

last: Le Bihan-Duval

first: Amélie

last: Juanchich


title: Galectin-1-RNA interaction map reveals its novel regulatory roles in angiogenesis

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Hyperactive angiogenesis contributes to the immunosuppressive microenvironment important for immunotherapy, and LGALS1-encoed galectin-1 can trigger vascular signaling programs and mediate anti-angiogenic treatment response. However, the mechanism of galectin-1 regulation of angiogenesis is poorly understood. Previous mRNA interactome studies suggested that galectin-1 associated with mRNAs. In this study, we applied the iRIP-seq methodology, an unbiased genome-wide approach to study the RNA binding profiles of galectin-1. The results demonstrate that galectin-1 interacted with a large population of mRNAs with a preferred location towards stop codon, and preferred motifs of UGCA/UGGA and GAGCAG motifs.  Galectin-1-bound mRNAs are enriched in cell cycle control and diverse basic biological processes, including its previously reported protein targets H-Ras and also T cell receptors TLR6. Glectin-1 significantly binds to genes in angiogenesis, which included the key pro-angiogenic growth factor VEGFA, angiogenic regulators EGR1 and LAMA5, suggesting that galectin-1 may regulate via its mRNA binding activity. The presented results uncover an previously unrecognized mRNA binding activity of galectin-1; further pursue of this activity could lead to knowledge important for developing therapeutic strategies against cancer and other diseases involved in aberrant angiogenesis.

overall_design: RIP-seq analysis of LGALS1 IP versus input in Hela cells

first: Jiajun

last: Wei


title: Identification of genes regulated by MYCN in retinoblastoma (RB) cell line, Y79.

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To determine the downstream genes regulated by MYCN in RB, MYCN was silenced in Y79  cell line, which expressed hign levels of MYCN, using two lentiviral shRNA constructs targetting MYCN.

overall_design: Agilent Human Whole Genome 8x60k Microarray: AMADID: 72363

first: Mamatha

last: Reddy

first: Swatishree

last: Sradhanjali


title: Effects and molecular regulation mechanisms of saline-alkali stress on the healthy grass carp [exp2]

status: Public on Oct 13 2021

city: wuhan

first: wu

middle: xiao

last: man

address: Donghu South Road

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary:
Purpose:Salinity is an important environmental factor that affects the physiological activities of fish. Flavobacterium cloumnare is a major aquaculture pathogen infecting various saltwater and freshwater fish. The goals of this study are investigating the mechanism of the immune responses to Flavobacterium cloumnare in grass carp under saline-alkali stress.
Methods: Grass carp individuals, averaging 12 cm in body length, were obtained from Duofu fish farm (Wuhan, China) and cultured at recirculating aquaculture system for 2 weeks before the experiment began. For the challenge, all grass carp were  randomly divided into three groups, and then cultured at saline-alkali water with the concentration of 0, 3‰ and 6‰. After 30 days, Groups of grass carp were were infected with 2 × 105 CFU/mL Flavobacterium cloumnare G4 strains for 3 h .Gills from each group at 24 hpi, 3dpi and 6dpi were collected. Total RNA of all samples was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's introduction. gill per group at 24 hpi and 48 hpi were rinsedRNA integrity was assessed using an Agilent 2100 bioanalyzer (Agilent, USA). Samples with RNA integrity numbers (RINs) ≥ 7.5 were subjected to cDNA library construction using TruseqTM RNA sample prep Kit (Illumina).
Results:A total of 27 were processed for transcriptome sequencing, generating 177.79Gb Clean Data. At least 5.73Gb clean data were generated for each sample with minimum 93.70% of clean data achieved quality score of Q30. Clean reads of each sample were mapped to specified reference genome. Mapping ratio ranged from 88.11% to 92.33%. The expression of genes was quantified and differentially expressed genes were identified based on their expression.Criteria for differentially expressed genes was set as Fold Change(FC)≥1.5 and Pvalue<0.05. Fold change(FC) refers to the ratio of gene expression in two samples. These DEGs were further processed for functional annotation and enrichment analysis.
Conclusions: Our study represents the immune response of zebrafish against Flavobacterium cloumnare infection in saline-alkali stress conditions, and reveal the discrepant expression pattern of NOD-like pattern recognition receptors in the gills.

overall_design: Total RNA was solated from gills of grass carp at 24 hpi, 3dp and 7dpi after cutured at saline-alkali water with the concentration of 0, 3‰ and 6‰ for 30 days

first: Hong

last: Fang

first: Xiao

last: Wu

first: Yuan

middle: Y

last: Yang

first: Ming

middle: X

last: Chang


title: Endothelial UCP2 regulates the neurogenic-to-astrogenic fate switch during brain development

first: Jianwei

last: Jiao

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose: To gain  futher insight into how endothelial UCP2 regulates the neurogenic-to-astrogenic fate switch ,RNA-seq was used to analyze the genome-wide changes resulting from isolated endothelial cells of E14.5 and E17.5 UCP2 endothelial conditional knock out mice and littermate wild-type.
Methods:  mRNA from E15 and E18 isolated endothelial cells of wild-type(WT) and UCP2f/f;Tie2-cre mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics
Results: Approximately  one thousand transcripts showed differential expression between the wild-type(WT) and UCP2ECKO mice brain cortex, with a fold change ≥2 and p value <0.05.Geneontology analysis of the up-regulated genes showed obvious enrichment of biological processes related to development process and regulation of cell communication.The down-regulated genes exhibited enrichment of biological processes related to cell fate commitment. These results reflected endothelial UCP2  plays  roles in cortex development.
Conclusions:  Endothelial UCP2 RNA-seq would provide a overall understanding how endothelial UCP2 regulates the neurogenic-to-astrogenic fate switch during brain development

overall_design: mRNA profiles of E15 and E18 wild type (WT) and UCP2ECKO mice were generated by deep sequencing, in triplicate,  using Illumina HiSeq 2500.

first: Wenwen

last: Wang


title: Profiling of mRNA transcriptomic changes using RNA-seq in postmortem putamen of subjects with alcohol use disorder

city: Boston

first: Huiping

last: Zhang

state: Massachusetts

address: 72 East Concord Street

department: Psychiatry

institute: Boston University School of Medicine

summary:
Purpose: The goal of this study to examine mRNA transcriptomic changes in reward-related brain regions of subjects with alcohol use disorder.
Methods: Total RNAs were extracted from postmortem putamen of 12 AUD and 12 control subjects. rRNA depletion RNA sequencing was performed and the sequence reads were processed using the bulk RNA-seq processing pipeline Pipeliner workflow (Federico et al. Front Genet 2019; 10, 614). AUD-associated mRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: Differentially expressed mRNAs (absolute FC>2.0 & P<0.05) were identified in postmortem putamen of subjects with alcohol use disorder (AUD).
Chronic alcohol consumption may alter mRNA transcriptome profiles in reward-related brain regions, resulting in alcohol-induced neuroadaptations.

overall_design: Cases and controls were matched by race, sex, age, etc.

first: Zhang

last: Huiping


city: chongqing

first: xiaofang

last: luo

address: 1 Youyi Road, Yuzhong District

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Chip-seq analyses of PPARγ bonded DNA fragments revealed that Arid5b, Rorb, Pank2 and Htr2c are the downstream target genes for PPARγ regulated adipogenesis in fetal preadipocyte.

overall_design: Chip-seq of  3T3-L1 preadipocytes and PPARγ-OE HTR8-Exos treated 3T3-L1 preadipocytes

first: Xiaofang

last: Luo


title: Expression data from C42B prostate cancer cell line treated with enzalutamide and/or sphingosine kinase inhibitor PF-543 or ABC294640

city: Darlinghurst

first: Hui-Ming

last: Lin

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary:
Epidemiological and molecular evidence indicate that sphingolipids may play a role in the resistance of prostate cancer to androgen receptor signalling inhibitors such as enzalutamide, through the metabolism of ceramide into sphingosine-1-phosphate (S1P) which activates specific G-protein coupled receptors present on cancer cells and immune cells. Sphingosine kinase inhibitors which prevent the production of S1P have anti-cancer effects in vitro and in animal models.
Our work showed that SPHK inhibitors can enhance the efficacy of enzalutamide in prostate cancer cell lines. We used microarrays to investigate the transcriptomic changes from the combination of enzalutamide with the SPHK1 inhibitor PF543, or SPHK2 inhibitor ABC294640, in C42B, one of the prostate cancer cell line.

overall_design: C42B cells were treated with vehicle control dimethyl sulfoxide (DMSO), enzalutamide, PF-543, ABC-294640, combination of enzalutamide with and PF-543, or combination of enzalutamide with ABC-294640. After 6 hours of treatment, RNA were extracted, processed and hybridised onto Affymetrix arrays.

first: Lisa

middle: G

last: Horvath


title: Profiling of mRNA transcriptomic changes using RNA-seq in postmortem amygdala of subjects with alcohol use disorder

summary:
Purpose: The goal of this study to examine mRNA transcriptomic changes in reward-related brain regions of subjects with alcohol use disorder.
Methods: Total RNAs were extracted from postmortem amygdala of 12 AUD and 12 control subjects. rRNA depletion RNA sequencing was performed and the sequence reads were processed using the bulk RNA-seq processing pipeline Pipeliner workflow (Federico et al. Front Genet 2019; 10, 614). AUD-associated mRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: Differentially expressed mRNAs (absolute FC>2.0 & P<0.05) were identified in postmortem amygdala of subjects with alcohol use disorder (AUD).
Chronic alcohol consumption may alter mRNA transcriptome profiles in reward-related brain regions, resulting in alcohol-induced neuroadaptations.


title: Single cell RNA sequencing of human failing heart

first: Shengshou

last: Hu

address: No.167 North Lish Road

institute: Fuwai Hospital

summary: we performed single cell RNA sequencing (scRNA-seq) in both normal and failed human heart.  CD45- cells in the myocardium and  immune cells (CD45+ cells) were isolated from myocardium and corresponding peripheral blood were sorted for scRNA-seq. Our findings were also validated with bulk RNAseq.

overall_design: Establishing a comprehensive cell atlas of immune cells in human heart failure at single cell level.

first: Jiangping

last: Song

first: Xueda


title: Profiling of mRNA transcriptomic changes using RNA-seq in postmortem prefrontal cortex of subjects with alcohol use disorder

summary:
Purpose: The goal of this study to examine mRNA transcriptomic changes in reward-related brain regions of subjects with alcohol use disorder.
Methods: Total RNAs were extracted from postmortem prefrontal cortex of 12 AUD and 12 control subjects. rRNA depletion RNA sequencing was performed and the sequence reads were processed using the bulk RNA-seq processing pipeline Pipeliner workflow (Federico et al. Front Genet 2019; 10, 614). AUD-associated mRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: Differentially expressed mRNAs (absolute FC>2.0 & P<0.05) were identified in postmortem prefrontal cortex of subjects with alcohol use disorder (AUD).
Chronic alcohol consumption may alter mRNA transcriptome profiles in reward-related brain regions, resulting in alcohol-induced neuroadaptations.


title: Transcriptome sequencing Analysis of hLFSCs with and without mechanical stress

city: Xining

first: Liu

last: Chenhao

state: Qinghai

address: Xinqiao Street

department: Orthopedic

institute: Qinghai Provincial People's Hospital

summary: Purpose:The goals of this study are to MS (mechanical stress) how to change the cellular pathway of hLFSCs (human ligament flavum stem cells). Methods: Extract hLFSCs from the ligament flavum of patients.Treat the cells with and without (in control)MS.Total RNA was extracted from cells with Tripure Isolation Reagent.Subsequently, RNA was purified through rRNA depletion and then subjected to cDNA synthesis and RNA amplification. Next, random hexamer primer cDNA libraries were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and sequenced on Illumina Hiseq 4000 sequencing platform (Illumina, San Diego, California, USA) following the manufacturer’s instructions for paired-end 150 bp reads (Lifegenes, Shanghai, China).

overall_design: mRNA sequence of hLFSCs with and without mechanical stress

first: Chenhao

last: Liu


title: Glioblastoma stem-like-cells

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

country: Germany

institute: Universitätsklinikum des Saarlandes

type: Methylation profiling by genome tiling array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of GBM Stem-like Cells Upon Extensive Culturing Time [RNA-Seq]

summary: Genome wide expression profiling of glioblastoma stem-like-cells to detect changes in the gene expression after long-time cultuing the cells.

overall_design: Examination of 7 GBM cell lines to detect evolved genes in culture

first: Ann-Christin

last: Nickel

first: Daniel

last: Picard


title: endometrial microbiome

first: CHAO

last: LI

address: No. 2699, West GaoKe Road

institute: Shanghai First Maternity and Infant Hospital

summary:
The gut-uterus axis plays a pivotal role in the pathogenesis of endometrial cancer (EC). However, the correlations between the endometrial microbiome and endometrial tumor transcriptome in patients with EC and the impact of the endometrial microbiota on hematological indicators have not been thoroughly clarified. In this prospective study, endometrial tissue samples collected from EC patients (n = 30) and healthy volunteers (n = 10) were subjected to 16S rRNA sequencing of the microbiome. The 30 paired tumor and adjacent nontumor endometrial tissues from the EC group were subjected to RNAseq.
Result: We found that Pelomonas and Prevotella were enriched in the EC group with a high tumor burden. Further transcriptome analysis identified 8 robust associations between Prevotella and fibrin degradation-related genes expressed within ECs.
Conclusions: Our results suggest that the increasing abundance of Prevotella in endometrial tissue combined with high serum DD and FDP contents may be important factors associated with tumor burden.

overall_design: A total of 60 samples including 30 paired tumor and adjacent nontumor endometrial tissues are analyzed.

first: Chao

last: Li

first: Ye

last: Gu

first: Qizhi

last: He

first: Jian

last: Huang

first: Yunfeng

first: Xiaoping

last: Wan

first: Yiran


title: Analysis of microRNA transcriptomic changes in ethanol-exposed human embryonic stem cell (hESC)-derived cortical interneurons using small RNA sequencing

first: Huiping

last: Zhang

summary:
Purpose: The goal of this study to use ethanol-exposed human embryonic stem cell (hESC)-derived neural cells as models to investigate microRNA expression changes in the brains of subjects with alcohol use disorder (AUD).
Methods: hESCs were differentiated into neural cells (mainly cortical interneurons), which were then cultured in media with or without ethanol (50-100 mM) for 7 days (by duplicate experiments). Total RNAs were extracted from hESC-derived neural cells (with or without ethanol exposure) for small RNA sequencing. The sequence reads were processed using the Comprehensive Analysis Pipeline for miRNA Sequencing Data (CAP-miRseq) workflow. Ethanol-induced miRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: A 7-day ethanol exposure led to differential expression of six miRNAs (absolute FC>2.0 & P<0.05) in hESC-derived cortical interneurons. Three miRNAs were upregulated (>2-fold increase & P<0.05), while three other miRNAs were downregulated (> 2-fold decrease & P < 0.05) due to ethanol exposure.
Conclusions: The hESC-derived neural cell model study can partially validate miRNA transcriptomic changes in postmortem brains of subjects with alcohol use disorder.

overall_design: hESC-derived neural cells exposed (or unexposed) to ethanol for 7 days


title: Immune profiling in mice treated with BCL2 or JAK1/2 inhibitors

city: Melbourne

first: Rachel

last: Koldej

address: 305 Grattan St

institute: Melbourne Health

summary: This study examined the impact of venetoclax or ruxolitinib on the immune profile of the bone marrow in treated mice showing venetoclax reduced expression of MHC-II and IFNg associated genes while ruxolitinib upregulated MHC-II and downregulated IFNg associated genes.

overall_design: The BCL2 inhibitor venetoclax and JAK1/2 inhibitor ruxolitinib (SelleckChem, Houston, TX) were used to treat C57BL/6 WT mice for two days.  Venetoclax (100 mg/ml) and its vehicle (60% phosal R 50 PG (Merck, Germany), 30% polyethylene glycol (PEG) 400 (Merck, Germany), 10% ethanol) were administered by oral gavage once daily for two days.  Ruxolitinib (180 mg/ml) and its vehicle (2% DMSO, 30% PEG 300 (Merck, Germany), ddH2O) were administered twice a day by oral gavage for two days. Total BM RNA was extracted from cohorts of mice (n=3-4) days 1, 3 and 7 post-drug treatment or from untreated controls using the Qiagen RNeasy Kit (Qiagen, Venlo, The Netherlands). Gene expression was determined using the NanoString Mouse Immunology Panel (NanoString Technologies, Seattle, WA) as per manufacturer’s instructions.  All raw data was reviewed, and all samples in downstream analysis had no quality control flags and detection of at least 20% of probes. All experiments were normalised and analysed using nCounter Advanced Analysis (version 2.0.115; NanoString Technologies).

first: Joanne

last: Davis


title: P16 positive microglia population identified in the aged mouse brain

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

summary: Senescent cells are in a state of permanent cell cycle arrest, which is mediated by the Cyclin Dependent Kinase (CDK)4/6 inhibitor p16. During ageing, p16-expressing (P16pos) cells accumulate in tissues and promote multiple age-related pathologies, including neurodegenerative diseases. We evaluated the accumulation and the phenotype of senescent cells in the aged brain with a transgenic reporter mouse (p16-3MR), which allows for isolation of P16poscells. First, we showed that the number of P16pos cells is significantly increased in old brains. Second, using bulk RNAseq, we demonstrated that P16pos cells express high levels of inflammatory and lysosomal genes. Third, using single-cell RNAseq, we identified P16pos brain cells as being primarily microglia. Interestingly, the transcriptional profile of P16pos microglia cells is distinct from cell type signatures associated with senescence or defined microglia populations. Taken together, our study provides evidence for the accumulation of a novel P16pos microglia population in the aging brain, which could result in loss of tissue homeostasis and contribute to brain dysfunction.

overall_design: Bulk RNAseq of RFPneg and RFPpos cells from brains from p16–3MR mice with a C57BL/6 background (n=5). Single-cell RNAseq of the total viable population brain cells and RFPpos brain cells from 5 mice pooled.

first: Nynke

last: Talma

first: Boshi

last: Wang

first: Bart

last: Eggen

first: Marco

last: Demaria


title: Profiling mRNA transcriptomic changes using Affymetrix Clarion D assay in 6 regions of postmortem brains of subjects with alcohol use disorder

summary:
Chronic alcohol consumption may alter mRNA transcriptomic changes in reward-related brain regions, leading to neuroadaptations and thus increased risk of AUD.
We used the Affymetrix Clariom™ D Assay Array to map mRNA transcriptome profiles in six reward-related regions of postmortem brains of AUD and control subjects and identified differentially expressed mRNAs.

overall_design: Total RNAs were extracted from tissue samples dissected from six regions (amygdala, caudate nucleus, cerebellum, hippocampus, prefrontal cortex, and putamen) of postmortem brains of 8 male patients with alcohol use disorder (AUD) and 8 male control subjects. Both AUD patients and control subjects were assessed with DSM-IV. The Affymetrix Clarion D microarray data was processed using the Expression Console (EC) software.

first: Zhang

last: Huiping


title: Single cell RNA sequencing for normal and diseased mouse femoral artery

city: Hangzhou

first: Qingbo

last: Xu

state: Zhejiang

address: 79 Qingchun Road

department: Department of Cardiology

institute: First Affiliated Hospital, Zhejiang University School of Medicine

summary: Endothelial cells play a critical role in multiple cardiovascular diseases. CD34+ cells are believed to be endothelial progenitors that have been used to treat cardiovascular disease. However, the exact identity and the role of CD34+ cells in vascular regeneration remains unclear.Here we performed single cell RNA sequencing to identify heterogeneous CD34+ cells serve as a contributor to endothelial regeneration.

overall_design: This entry contains 10x Single-cell RNA-seq data of all cells and FACS sorted CD34+ cells from normal C57BL6/J femoral arteries, and cells from normal, 2-week and 4-week guide-wire injured Cd34-CreERT2;R26-tdTomato femoral arteries.

first: Liujun

last: Jiang

first: Jiacheng

last: Deng

first: Ting

last: Chen


title: Profiling of miRNA transcriptomic changes using small RNA-seq in 8 regions of postmortem brains of subjects with alcohol use disorder

summary:
Purpose: The goal of this study to examine miRNA transcriptomic changes in reward-related brain regions of subjects with alcohol use disorder.
Methods: Total RNAs were extracted from 8 reward-related regions of postmortem brains of 12 AUD and 12 control subjects (8x24=192 tissue samples). Small RNA sequencing was performed and the sequence reads were processed using the Comprehensive Analysis Pipeline for miRNA Sequencing Data (CAP-miRseq) workflow. AUD-associated miRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: 19 differentially expressed mature miRNAs (absolute FC>2.0 & P<0.05) were identified in one or multiple brain regions
Chronic alcohol consumption may alter miRNA transcriptome profiles in reward-related brain regions, thus changing the expression of their target mRNAs and resulting in alcohol-induced neuroadaptations.


title: Thrombospondin-4 is a soluble dermal inflammatory signal that activates the fibroblast migration for skin regeneration and wound healing

city: Tartu

first: Mariliis

last: Klaas

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

summary: The present study aimed to investigate the role of Thbs4 in skin regeneration and elucidate its effects on cellular responses. Here we show that Thbs4 expression is upregulated in healing skin wounds and wound healing can be promoted by the application of recombinant Thbs4 protein. Thbs4 was shown to promote keratinocyte proliferation and fibroblast migration by activating β-catenin signalling cascade. This indicates that incorporating Thbs4 into novel wound healing therapies can be a promising therapeutic strategy for hard-to-heal chronic wounds.

overall_design: Changes in human primary skin fibroblast mRNA profiles in response to stimulation with recombinant Thbs4 protein

first: Viljar

last: Jaks


title: Profiling of mRNA transcriptomic changes using RNA-seq in postmortem cerebellum of subjects with alcohol use disorder

summary:
Purpose: The goal of this study to examine mRNA transcriptomic changes in reward-related brain regions of subjects with alcohol use disorder.
Methods: Total RNAs were extracted from postmortem cerebellum of 12 AUD and 12 control subjects. rRNA depletion RNA sequencing was performed and the sequence reads were processed using the bulk RNA-seq processing pipeline Pipeliner workflow (Federico et al. Front Genet 2019; 10, 614). AUD-associated mRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: Differentially expressed mRNAs (absolute FC>2.0 & P<0.05) were identified in postmortem cerebellum of subjects with alcohol use disorder (AUD).
Chronic alcohol consumption may alter mRNA transcriptome profiles in reward-related brain regions, resulting in alcohol-induced neuroadaptations.


title: Epigenome analysis of glioblastoma stem-like-cells after long time culturing [Methylation]

first: Marc

last: Remke

summary: Genome wide DNA methylation profiling of glioblastoma stem-like-cells was performed to detect changes during long time culturing. The Illumina Infinium MethylationEPIC Kit array was used to obtain DNA methylation profiles across approximately 850,000 CpGs. The samples are seven cell lines containing an early passage (x+0) and an later passage (x+30).

overall_design: Bisulphite converted DNA from the 12  samples were hybridised to the Illumina Infinium Methylation EPIC Kit array

first: Ann-Christin

last: Nickel

first: Daniel

last: Picard


title: Analysis of mRNA transcriptomic changes in ethanol-exposed human embryonic stem cell (hESC)-derived cortical interneurons using ribosome depletion RNA sequencing

first: Huiping

last: Zhang

summary:
Purpose: The goal of this study to use ethanol-exposed human embryonic stem cell (hESC)-derived neural cells as models to investigate mRNA expression changes in the brains of subjects with alcohol use disorder (AUD).
Methods: hESCs were differentiated into neural cells (mainly cortical interneurons), which were then cultured in media with or without ethanol (50-100 mM) for 7 days (by duplicate experiments). Total RNAs were extracted from hESC-derived neural cells (with or without ethanol exposure) for mRNA sequencing. The sequence reads were processed using the RNA-seq processing pipeline Pipeliner [Front Genet. 2019; 10:614] workflow. Ethanol-induced mRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: When the significance level was set at FC>2.0 & P<0.01, 19 coding genes showed differential expression, and all of them were downregulated after a 7-day ethanol exposure.
Conclusions: The hESC-derived neural cell model study can partially validate mRNA transcriptomic changes in postmortem brains of subjects with alcohol use disorder.


title: Profiling miRNA transcriptomic changes using Affymetrix miRNA4.0 in 6 regions of postmortem brains of subjects with alcohol use disorder

summary:
Chronic alcohol consumption may alter miRNA transcriptome profiles in reward-related brain regions. Given that miRNAs can regulate the expression of their target coding genes (or mRNAs) at the post-transcriptional level, alcohol-induced miRNA expression change may influence the expression of their targets mRNAs that are involved in alcohol use disorder (AUD)-related pathways, leading to increased risk of AUD.
We used the Affymetrix GeneChip™ miRNA 4.0 Array to map miRNA transcriptome profiles in six reward-related regions of postmortem brains of AUD and control subjects and identified differentially expressed miRNAs.

overall_design: Total RNAs were extracted from tissue samples dissected from six regions (amygdala, caudate nucleus, cerebellum, hippocampus, prefrontal cortex, and putamen) of postmortem brains of 8 male patients with alcohol use disorder (AUD) and 8 male control subjects. Both AUD patients and control subjects were assessed with DSM-IV. The Affymetrix miRNA4.0 microarray data was processed using the Expression Console (EC) software.


title: Profiling of mRNA transcriptomic changes using RNA-seq in postmortem caudate nucleus of subjects with alcohol use disorder

summary:
Purpose: The goal of this study to examine mRNA transcriptomic changes in reward-related brain regions of subjects with alcohol use disorder.
Methods: Total RNAs were extracted from postmortem caudate nucleus of 12 AUD and 12 control subjects. rRNA depletion RNA sequencing was performed and the sequence reads were processed using the bulk RNA-seq processing pipeline Pipeliner workflow (Federico et al. Front Genet 2019; 10, 614). AUD-associated mRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: Differentially expressed mRNAs (absolute FC>2.0 & P<0.05) were identified in postmortem caudate nucleus of subjects with alcohol use disorder (AUD).
Chronic alcohol consumption may alter mRNA transcriptome profiles in reward-related brain regions, resulting in alcohol-induced neuroadaptations.


title: Gene expression profile of K562 treated with the combination of imatinib and miR-342-5P

city: Taipei

first: Yilin

last: Chiu

address: No.161, Minquan E. Road 6th Sec., Neihu dist.,

department: Biochemistry

country: Taiwan

institute: National Defense Medical Center

summary: To determine the specific gene expression of imatinib in CML cells with or without miR-342-5P expression, gene array analysis was performed.

overall_design: K562 cells were transfected with miR-NEG or miR-342-5p 20 nM for 1 consecutive day pre-exposure followed by IM 0.5 μM exposure. Total RNA was extracted from each cell line 24 h after IM exposure and gene expression was compared between 4 groups, control (miR-NEG), miR-342-5P, miR-NEG+IM and miR-342-5P+IM.

first: Yi-Ying

last: Wu

first: Yuwen

last: Lin


title: RNA Sequencing reveals transcriptome profiling of HUVECs in response to NETs ± defibrotide

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: We reported the application of RNA sequecing to broadly understand the pathways associated with HUVECs exposed to vehicle, NETs, or NETs + defibrotide. We identified 440 differentially expressed genes (300 upregulated) in HUVECs upon NET stimulation as compared with vehicle. Conversely, there were 229 differentially expressed genes (192 downregulated) when the NETs + defibrotide group was compared to NETs alone.

overall_design: A human umbilic endothelial cell line (ATCC) was cultured and treated with the NET stimulus alone or the NET stimulus plus a drug (defibrotide).

first: Hui

last: Shi

first: Jason

middle: S

last: Knight

first: Dana

last: King

first: Karthik

last: Padmanabhan


title: RNAseq analysis of cochlear glial sphere and induced neurons transcriptomes from  SCDM, SCDM/FGF and FIBCL differentiation in vitro

city: Nanjing

first: zhen

last: chen

state: Jiangsu

address: 12 Xuefu-Road, Pukou District

department: Model Animal Research Center

institute: Nanjing university

summary: To evaluate the maturity under different induction conditions of induced neurons, we performed transcriptome sequencing analysis. Pearson correlation analysis showed that the expression profiles of neurons induced by SCDM and SCDM/FGF are relatively close to that of spheres, while the overall expression of small molecules iNs is quite different from the above three types of cells, which is more similar with the transcriptome expression of primary SGN. These results generally show that small molecules effectively promote the neural differentiation towards SGN.

overall_design: Examination of the gene expression pattern and neuronal maturation of small molecules FIBCL induced neuron from cochlear glial sphere

first: Guoqiang

last: Wan

first: Zhen


title: An enhancer-driven stem cell-like program mediated by SOX9 blocks intestinal differentiation in colorectal cancer

first: Nilay

last: Sethi

state: MA

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana Farber Cancer Institute

summary: This SuperSeries is composed of the SubSeries listed below.


title: The role of PARP-1 in estrogen-dependent transcription [RNA-seq]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Poly (ADP-ribose) polymerase-1 (PARP-1), a multifunctional chromatin-modulating protein, has gained considerable attention as a target for therapeutic inhibitors in breast cancers.  Accumulating evidence suggests a pathological role for PARP-1 in breast cancer through its effects on the transcription of tumor-related genes.  Here we report the role of PARP-1 in estrogen-dependent transcription in estrogen receptor alpha (ERα)-positive breast cancers.  Global nuclear run-on and sequencing (GRO-seq) and RNA-seq analyses suggest that PARP-1 controls the expression of estrogen-regulated genes in ER-positive (ER+) MCF-7 breast cancer cells.  Further, ChIP-seq analyses revealed that PARP-1 directly regulates the ligand-dependent binding of ERa and FoxA1 to a subset of its genomic binding sites.  Finally, we uncovered that the expression levels of the PARP-1 and estrogen coregulated gene set are enriched in luminal molecular-subtype of breast tumors and high PARP-1 expression in ER+ cases correlates with poor survival.  Additionally, treatment with PARP-1 selective inhibitors showed attenuated estrogen-dependent growth of ER+ breast cancer cells.  Taken together, the current study suggests that PARP-1 regulates critical molecular pathways that underlie proliferation of ER+ breast cancer cells.

overall_design: Using RNA-seq upon 17b-estradiol (E2) treatment in MCF-7 cells.

first: Shrikanth

last: Gadad

first: Cristel

middle: V

last: Camacho

first: Venkat

last: Malladi

first: Anusha

last: Nagari

first: Kraus

middle: W

last: Lee


title: RNA seq of H2O, glucose, mannose or galactose-treated Batrachochytrium salamandrivorans zoospores

city: Merelbeke

first: Yu

last: Wang

address: Salisburylaan 133, D5

country: Belgium

institute: Ghent University

summary: We report RNAseq data from B. salamandrivorans zoospores treated with different carbohydrates (glucose, mannose or galactose, 50 mM) or H2O as a control, for 1 hour. We found a selective upregulation of putative B. salamandrivorans virulence factors during initial contact with carbohydrates and galactose specifically.

overall_design: Total RNA was isolated from B. salamandrivorans zoospores treated with different carbohydrates. Therefore, zoospores were harvested from 175 cm2 cell culture flasks by replacing the TGhL broth with distilled water, which was filtered using a sterile mesh filter with pore size 10 µm. Six independent pools containing 4 x 10e7 zoospores were obtained (biological replicates). Per pool, the spores were divided in 4 eppendorfs (10e7 zoospores/eppendorf) which were treated for 1 hour at 15°C with H2O (control), 50 mM (α-D-galactose), 50 mM (α-D-glucose) or 50 mM (α-D-mannose). After 1 hour, the zoospores were centrifuged for 5 min at 3000 rpm at 15°C to remove the supernatant, after which RNA was extracted using the RNeasy mini kit (Qiagen). The RNA was treated with Turbo™ DNase, following the manufacturer's instructions. RNA degradation and contamination was monitored on 1% agarose gels. The RNA purity was checked using the NanoPhotometer® spectrophotometer . Finally, the RNA integrity and quantitation were assessed using the RNA Nano 6000 assay kit of the Bioanalyzer 2100 system.

first: An

last: Martel

first: Frank

last: Pasmans

first: Moira

last: Kelly

first: Elin

last: Verbrugghe


title: Comparison of human BCP-ALL MLL-r and normal CD19+CD10+ precursor B-cell transcriptomes

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: B-cell precursor acute lymphoblastic leukemia (pre-B ALL) with mixed-lineage leukemia gene rearrangement (MLL-r) is a poor-prognosis subtype for which additional therapeutic targets are needed. We evaluated the glycomes, transcriptomes and proteomes of the same samples using only about 10^6 cells for each assay. We found that the expression of many genes involved in glycosylation differ between MLL-r cells and normal controls: 61 of the 221 human glycosyltransferases were differentially expressed in MLL-r cells. The leukemia cell glycome and many proteins associated with glycan biosynthesis were also significantly changed compared to normal control precursor B-cells, indicating that the malignant phenotype of these cells could be regulated by such changes.

overall_design: Four bone marrow samples from different donors depleted of CD34+ stem cells were used to isolate normal healthy precursor CD19+CD10+ B-cells. Red blood cells were removed from three leukemic pre-B ALL MLLr bone marrow samples before RNA isolation.

first: Nora

last: Heisterkamp

first: Hisham

last: Abdel-Azim

first: Eun-Ji

last: Joo

first: Lu

last: Yang


title: GRHL3 activates FSCN1 to relax cell adhesions between migrating keratinocytes in the wound front

city: Irvine

first: Ghaidaa

last: Kashgari

address: 250 sprague Hall

institute: University of California Irvine

summary: identify an underlying mechanism a new pathway where GRHL3 activates the Fscn1 gene to effect cell-cell loosening in the migrating wound front

overall_design: Transcriptomic analysis of wounded and unwounded keratinocytes

first: Bogi

last: Andersen


title: CD127+CD94+ innate lymphoid cells expanded in Crohn’s disease patients highly express granulysin and perforin

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

institute: Utrecht University

summary: Controversy in the identity and distinction of helper ILC1s and NK cells exist due to overlapping markers and the use of different gating strategies by distinct groups. Recently we identified cytotoxic ILC3s characterized by expression of CD94. Here we analyzed the full spectrum of CD127+ ILCs and NK cells in intestinal lamina propria from healthy donors and Crohn’s disease patients and identified two populations of CD127+CD94+ ILCs, designated A and B that could be distinguished on expression of CD117, CD18 and cytotoxic molecules. Population B highly expressed granulysin, a cytotoxic molecule linked to bacterial lysis and/or chemotaxis of monocytes. Granulysin protein was amply secreted by population B cells upon stimulation with IL-15. Activation of population B in the presence of TGF-β strongly reduced the expression of cytotoxic effector molecules of population B. Strikingly, samples from individuals that suffer from active Crohn disease displayed dramatically enhanced frequencies of granulysin expressing effector CD127+CD94+ ILCs compared to non-inflamed controls.

overall_design: Single cell sequencing of human ILC from the gut of Crohn's disease patients

first: Lisette

last: Krabbendam

middle: A

first: Chantal

last: Kradolfer

first: Nienke

middle: J

last: Haverkate

first: CJ

last: Buskens

first: WA

last: Bemelman

first: Jochem

middle: H

last: Bernink

first: Hergen

last: Spits


title: The role of PARP-1 in estrogen-dependent transcription

first: W. Lee

last: Kraus

overall_design: Refer to individual Series


title: Macrophage-Mediated Bone Formation of Scaffolds Modified with MSC-derived Extracellular Matrix Depends on Migration Inhibitory Factor Signaling Pathway

city: Chongqing

first: Moyuan

last: Deng

state: Chongqing

address: 30 Gao tanyan Street

department: Southwest hospital

institute: Army medical university

summary: Recently the role of macrophages on osteogenesis of mesenchymal stem cells (MSCs) is brought to focus. On the other hand, the cross-talk between macrophages and MSCs confirms that the paracrine molecules derived from macrophages are also carefully regulated by MSCs. Human umbilical cord mesenchymal stem cells (hucMSCs) could reduce secretions of inflammatory factors from macrophages for improving injury healing. hucMSC-derived extracellular matrix (hucMSC-ECM) exhibit nature similar to hucMSCs. It has been demonstrated that hucMSC-ECM possess considerable effects on reducing inflammatory response of macrophages, while the role of hucMSC-ECM on the expression of macrophage-derived paracrine osteogenic molecules is unclear. Here, we presented the decalcified bone scaffolds modified by hucMSC-derived extracellular matrix (DBM-ECM) maintaining multiple soluble cytokines including macrophage migration inhibitory factor (MIF). Compared with DBM, the DBM-ECM scaffolds induced bone formation in a macrophage-depending manner by an improved heterotopic ossification in SCID mice with or without macrophage depletion. Macrophage cocultured with the DBM-ECM expressed four osteoinductive cytokines (BMP2, FGF2, TGFβ3 and OSM), which were screen out by RNA sequencing, qPCR and western blot. The conditioned medium from macrophages cocultured with the DBM-ECM improved osteogenic differentiation of hBMSCs and activated CD74/CD44 signal transduction including phosphorylation of P38 and dephosphorylation of c-jun. Furthermore, the inhibitory effects of the DBM-ECM scaffolds with knockdown of MIF on osteogenesis in vitro and in vivo revealed that macrophage-mediated osteogenesis depends on MIF/CD74/ P38 signal transduction. This study indicates the coordinated crosstalk of macrophages and MSCs play a key role on bone regeneration induced by the DBM-ECM, with the emphasis on the constructing macrophage-derived osteoimmunological microenvironment.

overall_design: mRNA profiles of Thp-1 derived macrophages cocultured with DBM and DBM-ECM for 3 and 7days.

first: Jiulin

last: Tan


title: Long-term metabolic effect of chronic variable stress on liver function and the role of FGF21

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

summary: Chronic stress disorders lead to metabolic complications, including hepatic lipid accumulation. Here we address the role of FGF21 in the hepatic metabolic regulation in a mouse model for chronic variable stress (Cvs). Global FGF21KO and WT mice show an intact stress response with short-term Cvs induced alterations in hepatic lipid metabolism, mitochondrial function and gene expression. Hepatic steatosis is found with the highest significance in enrichment analyses of hepatic transcriptome data, with PPARa and SREBP-1 as main upstream regulatory molecules, which are directly associated to FGF21. After 3 months recovery, stress-related metabolic improvements are not visible in FGF21KO mice in contrast to WT mice, indicating the crucial role of FGF21 in the post-stress metabolic adaptations. Overall, we suggest that Cvs-induced gene regulation determines the metabolic late effects after stress. Furthermore, FGF21 is a key player in the protection from stress-induced hepatic lipid accumulation.

overall_design: Wildtype (WT; FGF21+/+) and Fgf21 knockout  (FGF21KO; FGF21-/-) (doi:https://doi:10.1210/en.2009-0119) male mice were stressed with our Cvs protocol as previously described (doi:https://doi.org/10.1016/j.molmet.2018.06.012).or left untreated (Ctrl). Transcriptome analyses (MTA array, Affymetrix) was performed in Ctrl and Cvs liver biopsies of each genotype. Mice were phenotyped for body composition, serum analyses, physiological tolerance tests and mitochondrial function, both immediately after stress and after 3 month recovery to determine longitudinal metabolic stress adaptation and the role of FGF21 in this context.

first: Matthias

last: Dille

first: Joerg

last: Kotzka


title: Dual checkpoint blockade of CD47 and PD-L1 using a novel affinity-tuned bispecific antibody maximizes anti-tumor immunity (NanoString)

city: San Diego

first: Wenjing

last: Yanf

state: CA

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

summary: A novel affinity-tuned dual-checkpoint bispecific antibody with potent PD-L1 and moderate CD47 affinity was designed to improve the selectivity to TME and thus enhance antitumor immunity and efficacy. The gene expression analysis using Nanostring platform was performed to examine the immune cell modulation in TME following the CD47/PD-L1 bispecific treatment.

overall_design: MC38 tumor-bearing C57/BL6 mice were treated with vehicle control, aCD47, aPD-L1 monotherapy, their combination, or the bispecific antibody every 3 to 4 days starting at day 10 post-tumor implant. Tumors were harvested at day 20 or day 24 and preared for gene expression analysis by Nanostring platform (n = 7~9 mice/group).

first: Shih-Hsun

last: Chen

last: Yang


title: ZBP1-MLKL-dependent Necroptosis Triggers STING-mediated Cytosolic DNA Sensing and Promotes Antitumor Immunity of Radiation

city: Shanghai

first: Liufu

address: Room 1002, West #5 Building, 280 South Chongqing Road, Shanghai 200025, China

institute: Shanghai Institute of Immunology; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine

summary: Ionizing radiation promotes cytosolic DNA sensing and consequent antitumor immune responses. But how tumor cell-intrinsic cytosolic DNA sensing is initiated by radiation remains poorly defined. Here, we demonstrated that STING-mediated type I interferon production in tumor cells after radiation relied on the engagement of MLKL-mediated necroptosis, which was elicited by the ZBP1-RIPK3 signaling axis. Physiologically, tumor cell-intrinsic ZBP1-MLKL cascade augmented antitumor immune responses after radiation largely by regulating STING signaling. Mechanistically, ZBP1-MLKL-dependent necroptosis maintained the enrichment of mitochondria DNA inside the cytosol of tumor cells after radiation in a cell-density dependent fashion, contributing to type I interferon responses. In contrast, ablation of caspase-8 unleashed ZBP1-MLKL cascade to gain enhanced cytosolic DNA sensing, and in turn potentiated therapeutic effects of radiation. Thus, our findings uncover an unanticipated mechanism that ZBP1-MLKL-dependent necroptosis drives cytosolic DNA sensing-mediated antitumor immunity after radiation, and provide new strategy to improve radiotherapy by inhibiting caspase-8 cascade.

overall_design: WT-MC38 (CRISPR-Ctrl) or MLKL-KO MC38 (MLKL-gRNA3) tumor cells were subjected to single fraction of X-ray (15 Gy). 60 hours later, total RNA from each sample was extracted using Trizol Reagent following standard protocols and mRNA sequencing was performed.

first: Yuanqin

first: Meng

last: Wu

first: Dongqing

last: Cao


title: MicroRNA-21-induced loss of Junctional Adhesion Molecule-A promotes activation of oncogenic pathways, progression and metastasis in colorectal cancer

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: Junctional adhesion molecules (JAMs) play a critical role in cell-cell interactions, cell permeability, polarity and migration. Gene expression and proteomic assays were used to define down-stream effectors of JAM-A dysregulation in colorectal cancer.

overall_design: RNA was extracted from JAM-A knockdown and ctrl cell lines (3 ctrl, 3 shRNA)

first: Nicola

last: Valeri


title: Silencing of circRNA Igf1r plays a protective role in neuronal injury via regulating astrocyte polarization during epilepsy

city: Wuhan

first: Lin

last: Shao

address: Donghu Rd185#, Wuhan, Hubei

institute: Wuhan University

summary: To identify epilepsy-related circular RNAs, we used three mice brain tissues of status epilepticus models and paired control brain tissues for RNA sequencing. Differential expressions of circRNAs were then analyzed.

overall_design: CircRNA profile of 3 paired brain tissue of mice with 4-aminopyridine induced status epilepticus models and control mice


title: Profiling of mRNA transcriptomic changes using RNA-seq in postmortem hippocampus of subjects with alcohol use disorder

city: Boston

first: Huiping

last: Zhang

address: 72 East Concord Street

institute: Boston University School of Medicine

summary:
Purpose: The goal of this study to examine mRNA transcriptomic changes in reward-related brain regions of subjects with alcohol use disorder.
Methods: Total RNAs were extracted from postmortem hippocampus of 12 AUD and 12 control subjects. rRNA depletion RNA sequencing was performed and the sequence reads were processed using the bulk RNA-seq processing pipeline Pipeliner workflow (Federico et al. Front Genet 2019; 10, 614). AUD-associated mRNA transcriptomic changes were analyzed by the Limma-Voom method.
Results: Differentially expressed mRNAs (absolute FC>2.0 & P<0.05) were identified in postmortem hippocampus of subjects with alcohol use disorder (AUD).
Chronic alcohol consumption may alter mRNA transcriptome profiles in reward-related brain regions, resulting in alcohol-induced neuroadaptations.

overall_design: Cases and controls were matched by race, sex, age, etc.

first: Zhang

last: Huiping


title: FOXR2 stabilizes MYCN protein and identifies non-MYCN-amplified neuroblastoma patients with unfavorable outcome

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

summary:
The stabilization of MYCN by FOXR2 represents an alternative mechanism to MYCN amplification to increase MYCN protein levels. As such, FOXR2 expression identifies another subset of neuroblastoma patients with unfavorable clinical outcome.
Background: Clinical outcomes of neuroblastoma patients range from spontaneous tumor regression to fatality. Hence, understanding the mechanisms that cause tumor progression are crucial for the treatment of patients. In this study, we show that FOXR2 activation identifies a subset of neuroblastoma tumors with unfavorable outcome and we investigate the mechanism how FOXR2 relates to poor outcome in patients.

overall_design: Total RNAs isolated from SK-N-AS and SK-N-FI cells transduced with inducible lentiviral constructs expressing either FOXR2 shRNA or scrambled shRNA were analyzed on human Affymetrix 133plus2.0 arrays

first: Felix

last: Schmitt-Hoffner


title: Tumor-reactive tissue resident memory T cells, regulatory T cells and prognosis in early luminal-like breast cancer

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

summary: Luminal-like breast cancer (BC) constitutes the majority of BC subtypes, but, differently from highly aggressive triple negative breast cancer (TNBC), is poorly infiltrated by the immune system. The quality of the immune infiltrate in luminal-like BCs has been poorly studied, thus a biological basis for the further investigation of immunotherapeutic strategies is missing. By using high-dimensional single-cell technologies, we identified heterogeneous behavior within the tissue-resident memory CD8+ T (Trm) cells infiltrating luminal-like tumors. We defined that a subset of CD127- CD39hi Trm cells is preferentially present in the tumor compared to the adjacent normal breast tissue or peripheral blood, displayed enhanced effector functions compared to the CD127+ CD39lo Trm counterpart, and was specifically associated with positive prognosis. Nevertheless, the prognostic benefit was lost in the presence of highly-suppressive CCR8hi ICOShi IRF4+ effector Tregs. Our results suggest that combinatorial strategies aiming at boosting Trm function while relieving from Treg-mediated immunosuppression are needed to achieve proper tumor control in luminal-like BCs.

overall_design: RNA-Seq profiling of CD127+ CD39low and CD127- CD39high CD8+ Trm cells

first: Agnese

last: Losurdo

first: Caterina

last: Scirgolea

first: Giorgia

last: Alvisi

first: Emilia

first: Enrico

last: Lugli


title: Stable overexpression of PPP2R3B in melanoma cell lines

city: London

first: Veronica

last: Kinsler

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Stable overexpression of PPP2R3B in the melanoma cell lines, SKMEL2 and SKMEL30

overall_design: Cells anlaysed un-induced and following overexpression PPP2R3B at 6h and 18h


title: RNA-Seq from zebrafish adult tissues

city: Vienna

first: Luis Enrique

last: Cabrera Quio

address: Campus Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

summary: The goal of this study was to profile transcript expression levels across zebrafish adult tissues.

overall_design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.

first: Carina

last: Pribitzer

first: Luis

first: Andrea

last: Pauli


title: Mitochondrial Dysfunction Induces Epigenetic Dysregulation by H3K27 Hyperacetylation to Perturb Active Enhancers in Parkinson’s Disease Models

city: Baltimore

first: Zhibin

last: Wang

state: MD

address: 615 N Wolf Steet

department: Environmental Health and Engineering

institute: Johns Hopkins University

summary: We aim to explore the predominant mitochondrial dysfunctions in PD, with a focus on how altering the histone code contributes to PD pathogenesis. We employ a multidisciplinary approach to convincingly demonstrate that neurotoxicant exposure- and genetic mutation-driven mitochondrial dysfunction share a common mechanism of epigenetic dysregulation. Under both scenarios, lysine 27 acetylation of likely variant H3.2 (H3.2K27ac) increased in dopaminergic neuronal models of PD, thereby opening that region to active enhancer activity via H3K27 hyperacetylation. These vulnerable epigenomic loci represent potential transcription factor motifs for PD pathogenesis. Our results reveal an exciting axis of ‘exposure/mutation-mitochondrial dysfunction-metabolism-H3K27ac-transcriptome’ for PD pathogenesis. Collectively, the novel mechanistic insights presented here interlinks mitochondrial dysfunction to epigenetic transcriptional regulation in dopaminergic degeneration as well as offer potential new epigenetic intervention strategies for PD.

overall_design: We performed genome-wide ChIP-Seq characterization of H3K27ac as well as transcriptome profiling in dopaminergic neurons whose mitochondria had been impaired either by exposure to a neurotoxic pesticide or by genetic modifications.

first: Minhong

last: Huang

first: Dan

last: Lou

first: Adhithiya

last: Charli

first: Dehui

last: Kong

first: Huajun

last: Jin

first: Vellareddy

last: Anantharam

first: Arthi

last: Kanthasamy

first: Anumantha


title: Impact of aging on diurnal gene expression in immune cells

city: Stanford

first: Connie

last: Tsai

address: 1201 Welch Rd

institute: Stanford University

summary: Transcriptomic analysis of macrophages harvested over the circadian day from young and aged mice reveals a loss of temporal synchrony in rhythmic gene expression with aging.

overall_design: Macrophages from young versus aged mice were harvested at ZT 0, 4, 8, 12, 16, 20, 24 for transcriptomic analysis

first: Katrin

last: Andreasson


title: Investigation of gene-expression profile of high immune-competent pigs

city: Tsukuba

first: Hirohide

last: Uenishi

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary: Transcriptional profiling of macrophages derived from immune-selected (phagocytosis, complement activity in the alternative pathway, and  antibody response after vaccination with swine erysipelas) in comparison with those from normal pigs

overall_design: Changes of gene expression of macrophages stimulated with lipid A were detected in comparison with unstimulated macrophages, and profiles of the changes were compared between macrophages derived from immune-selected and normal pigs.

first: Hiroki

last: Shinkai

first: Toshimi

last: Matsumoto


title: A comparison of alternative mRNA splicing in the CD4 and CD8 T cell lineages

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

institute: St Vincent's Institute of Medical Research

summary: We consturcted a full-length transcript reference of CD4SP and CD8SP T cells using TGS (PacBio) data.  We then used SGS (Illumina) CD4SP and CD8SP data to quantify isoform expressions and study alternative splicing patterns  against the full-length transcript reference between CD4SP and CD8SP cells.

overall_design: Constructed full-length trasncript reference and analysed alternative splicing events in CD4SP and CD8SP T cells with TGS (PacBio) long-read and SGS (Illumina) short-read data. PacBio long-read and Illumina short-read libraries were constructed for CD4SP and CD8SP cells.


title: The role of PARP-1 in estrogen-dependent transcription [ChIP-seq]

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Poly (ADP-ribose) polymerase-1 (PARP-1), a multifunctional chromatin-modulating protein, has gained considerable attention as a target for therapeutic inhibitors in breast cancers.  Accumulating evidence suggests a pathological role for PARP-1 in breast cancer through its effects on the transcription of tumor-related genes.  Here we report the role of PARP-1 in estrogen-dependent transcription in estrogen receptor alpha (ERα)-positive breast cancers.  Global nuclear run-on and sequencing (GRO-seq) analyses suggest that PARP-1 controls the expression of estrogen-regulated genes in ER-positive (ER+) MCF-7 breast cancer cells.  Further, ChIP-seq analyses revealed that PARP-1 directly regulates the ligand-dependent binding of ERa and FoxA1 to a subset of its genomic binding sites.  Finally, we uncovered that the expression levels of the PARP-1 and estrogen coregulated gene set are enriched in luminal molecular-subtype of breast tumors and high PARP-1 expression in ER+ cases correlates with poor survival.  Additionally, treatment with PARP-1 selective inhibitors showed attenuated estrogen-dependent growth of ER+ breast cancer cells.  Taken together, the current study suggests that PARP-1 regulates critical molecular pathways that underlie proliferation of ER+ breast cancer cells.

overall_design: Performed ChIP-seq (ERa, FoxA1 and H3K27ac) upon vehicle, 17b-estradiol (E2) treatment in MCF-7 cells.

first: Shrikanth

last: Gadad

first: Cristel

last: Camacho

first: Venkat

last: Malladi

first: W

middle: L


title: Transcriptomic changes induced by FLIL33 overexpression, stimulation with TGF-beta, and their combination in primary human lung fibroblasts

first: JP

last: Courneya

state: United States of America

address: 685 W Baltimore St., HSF2 Room 480

institute: University of Maryland, Baltimore

summary: RNA-Seq of normal adult human lung fibroblasts

overall_design: Normal human lung fibroblasts from an adult donor were electroporated with either FLIL33-encoding or a control non-coding (NULL) plasmids, and, 24 h later, either stimulated or not with rhTGF-beta. Analyses were performed 24 h and 48 h later.

first: Sergei

last: Atamas

first: Irina

last: . Luzina


title: Myeloid amino acid metabolism supports solid tumor malignancy

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

summary:
Cancer immunosuppression involves cellular pathways appropriated by tumors to escape immune surveillance but are normally required for tissue homeostasis and repair, self-tolerance, and successful transplantation. Among these pathways, enzymes that degrade tryptophan and arginine are thought to suppress activated T cells in the tumor microenvironment and are therefore attractive drug targets. However, how amino acid metabolism controls the development and progression of cancer has remained elusive, since commonly used implantable tumor models may not faithfully recapitulate the complex cellular and biochemical interactions within tumor microenvironments. To address this, we generated a novel, penetrant autochthonous model of neuroblastoma to accurately quantify tumor growth non-invasively and simultaneously genetically manipulate the enzymes that mediate tryptophan and arginine metabolism, and the cells that express them. We established that tumor development and growth were dependent on infiltrating CCR2+ bone marrow-derived myeloid cells but independent of Stat6-dependent ‘M2’ macrophages. Macrophages can modulate CD4+ T cell activation, proliferation, and differentiation by consuming amino acids and forcing the T cells to remain in the G1 phase of the cell cycle. Indeed, we found that CD4+ T cells deprived of arginine increased Foxp3 expression and adopted a unique regulatory-like phenotype. Notably, depletion of CD4+ T cells like CCR2+ macrophages, virtually eliminated tumor formation. When rare tumors did form in CD4-depleted mice, they contained Foxp3+ CD8 T cells, suggesting regulatory T cell activity is a fundamental requirement for tumor development. When we ablated macrophage arginase 1 (Arg1), an enzyme that locally consumes arginine, in the tumor-prone background, almost no tumors were observed. Therefore, Arg1 and arginine metabolism form a pro-tumor pathway. We extended these findings to two pathways of programmed myeloid tryptophan metabolism (IDO1, IDO2, IL4i1). Like Arg1, expression of these enzymes was confined to myeloid cells in humans and mice, and each enzyme was independently essential for tumor formation and growth. The protective effects of genetic ablation of each myeloid amino acid pathways uniformly occurred early in tumor formation, arguing that a network of immune cells controlled by myeloid amino acid metabolism and CD4+ T cells is important for the origins of a pro-tumor environment. Our results establish an unappreciated potency of macrophage amino acid metabolism in promoting malignancy, and suggest that these pathways can be disabled by targeting of myeloid amino acid metabolism.
OVA-specific CD4+ T cells were stimulated with peptide in the presence of APCs (CD3-depleted splenocytes) either in control complete RPMI-1640 (containing 10% dialyzed FBS) or in RPMI-1640 (containing 10% dialyzed FBS) containing 1% of the normal arginine levels (12uM) to characterize the effects of limited arginine availability on gene expression.

overall_design: Spleens and non-mesenteric lymph nodes were isolated from six OT II transgenic mice, and single cell suspensions were obtained by grinding through a 70-μm nylon mesh. Red blood cells were removed with RBC Lysis buffer (BioLegend) prior to purification. Antigen-presenting cells (APCs) were obtained by using the CD3ϵ MicroBead Kit (Miltenyi) according to the manufacturer's instructions. Purified CD4+ populations were obtained by negative selection. Cells were incubated with biotinylated anti-CD45R (B220, clone RA3-6B2), anti-I-A/I-E (clone M5/114.15-2), anti-CD11b (clone M1/70), anti-CD49b (clone DX5), and anti-CD8α (clone 53-607) (BioLegend). Cells were washed and incubated with streptavidin microbeads (Miltenyi), and then washed and passed over a magnetic column (Miltenyi). Purified T cells were resuspended in the appropriate medium given their respective treatment: RPMI-1640 (containing 10% dialyzed FBS) for 3 control samples, and RPMI-1640 (containing 10% dialyzed FBS) containing 1% of the normal arginine levels (12uM) for 3 treatment samples.

first: Lee

last: Van de Velde

middle: C

first: Peter

last: Murray

first: Paul

last: Thomas


title: Differential Lysotracker Uptake Defines Two Populations of Distal Epithelial Cells in Idiopathic Pulmonary Fibrosis

status: Public on Oct 12 2021

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: For this project alveolar epithelial type-II cells (AT-II) were FACS sorted from 8 donor lungs and 6 fibrotic lungs. The main goals of this experiment is to identify differences in transcriptional programms in AT-II cells from human donor and IPF patients.

overall_design: A total of 14 independent samples (8 from donor lungs, 6 from IPF lungs) were hybridized on Agilent Whole-transcriptome arrays.

first: Roxana

last: Wasnik


title: A transcriptomic analysis of primary fibroblasts isolated from young donors identifies a subset of donors displaying features of early senescence

city: Val-de-Reuil

first: Cécilia

last: Brun

address: Campus de Maigremont

department: Translational Science - Essential Health

country: France

institute: Johnson & Johnson Santé Beauté France

summary: Even though its development starts early in utero, neonatal skin is still immature at birth relative to adult and undergoes a maturation process extending to the first years of life. It is now established that stratum corneum is thinner and dryer, and that skin contains less natural moisturizing factors and lipids in newborns compared to children and adults. Moreover, it has been shown that skin surface area expansion is not linear throughout life and is peaking perinatally, suggesting that baby skin has a higher epidermal cellular turnover. Despite growing resources showing differences between adult and infant skin physiology, molecular and metabolic specificities of baby skin are still poorly understood. To address this critical knowledge gap, we performed an integrative transcriptomic and metabolomic study comparing human primary keratinocytes from babies and adults. Based on state-of-the-art integrative frameworks, our analyses revealed a major shift in the global energetic metabolism in baby keratinocytes compared to adults, highlighting increased amino acid metabolism and mitochondrial oxidative phosphorylation in baby cells to fuel TCA cycle, while showing glycolysis as the major cell energy source in adult cells.

overall_design: The proliferation potential of fibroblasts isolated from young donors was measured and compared to the one of cells isolated from the older group. Two subsets of donors were evidenced in the younger group: the first one with high proliferative (HP) capacities, the second one with significantly lower proliferative (LP) capacities, similar to the one of the older group. To further investigate the differences between the two subsets of young donors, a transcriptomic profiling was performed on fibroblasts from both young subgroups.

first: Pierre

middle: F

last: Roux

first: Thierry

last: Oddos


title: Gene expression of Treponema pallidum: in vitro vs. in vivo

city: Houston

first: Bridget

middle: Diane

last: De Lay

address: 6431 Fannin St., MSB 2.121

department: Pathology and Laboratory Medicine

institute: University of Texas McGovern Medical School

summary: Treponema pallidum ssp. pallidum, the causative agent of syphilis, can now be cultured continuously in vitro utilizing a tissue culture system, and the multiplication rates are similar to those obtained in experimental infection of rabbits. In this study, the RNA transcript profiles of the T. pallidum Nichols during in vitro culture and rabbit infection were compared to examine whether gene expression patterns differed in these two environments. To this end, RNA preparations were converted to cDNA and subjected to RNA-seq using high throughput Illumina sequencing; reverse transcriptase quantitative PCR was also performed on selected genes for validation of results. The transcript profiles in the in vivo and in vitro environments were remarkably similar, exhibiting a high degree of concordance overall. However, transcript levels of 94 genes (9%) out of the 1,063 predicted genes in the T. pallidum genome were significantly different during rabbit infection versus in vitro culture, varying by up to 8-fold in the two environments. Genes that exhibited significantly higher transcript levels during rabbit infection included those encoding multiple ribosomal proteins, several prominent membrane proteins, glycolysis-associated enzymes, replication initiator DnaA, rubredoxin, thioredoxin, two putative regulatory proteins, and proteins associated with solute transport. In vitro cultured T. pallidum had higher transcript levels of DNA repair proteins, cofactor synthesis enzymes, and several hypothetical proteins. The overall concordance of the transcript profiles may indicate that these environments are highly similar in terms of their effects on T. pallidum physiology and growth, and may also reflect a relatively low level of transcriptional regulation in this reduced genome organism.

overall_design: Two set of three in vitro culture samples (for a total of 6 in vitro samples) were compared to samples collected from two New Zealand white rabbits.

middle: D

first: Todd

last: Cameron

first: Nicholas

middle: R

first: Steven

last: Norris

first: Diane

last: Edmondson


title: Genome-wide mRNA profiling identifies X-box-binding protein 1 (XBP1) as an IRE1 and PUMA repressor

city: GDANSK

first: Rafal

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

summary: Previous studies suggested that XBP1s is important in deciding cell fate during the UPR, however, the mechanistic details of how it modulates this transition are limited. To search for XBP1s transcriptional targets, we utilized an XBP1s-inducible human cell line to limit XBP1 expression in a controlled manner.

overall_design:
Examination of XBP1s and XBP1u transcriptional activity in dedicated inducible HeLa cell lines.

GRANT: This research was funded by National Science Center "OPUS" Program under contract UMO-2020/37/B/NZ3/00861 to Rafal Bartoszewski


title: Gene Expression Profile of Diffuse Large B-Cell Lymphoma Cells upon inhibition of PIM kinanses

city: Warszawa

first: Michal

last: Pawlak

address: Indiry Gandhi 14

department: Department of Experimental Hematology

institute: Institute of Hematology

summary: Gene expression profiling of diffuse large B-cell lymphoma (DLBCL)-derived cell lines exposed to the pan-PIM inhibitor MEN1703 was performed to investigate transcriptional consequences of PIM kinase inhibition in DLBCL and to identify treatment-related changes in the signalling pathways.

overall_design: Cells at density 0.5x10E6/ml were treated in biological replicates with DMSO (control) alone or 1.5 µM MEN1703 for 24 hours.

first: Maciej

last: Szydlowski

first: Przemyslaw

last: Juszczynski


title: Direct Coculture of hPSC-derived Cardiac Progenitor Cells with Epicardial cells induces Cardiomyocyte proliferation and ventricular specification

city: Madison

first: Martha

last: Floy

state: Wi

address: 1415 Engineering Hall

country: USA

institute: University of Wisconsin-Madison

summary: Epicardial cells (EpiCs) form the epicardium, the outer layer of the heart surrounding the myocardium.  During development and in response to injury EpiCs undergo an epithelial to mesenchymal transition (EMT) migrating inward to create fibroblasts and smooth muscle cells in the myocardium. EpiCs have been shown to be necessary for proper myocardium formation, yet little is known about crosstalk between EpiCs and cardiomyocyte (CMs) and the potential impact of EpiCs on CM maturation. Here, we differentiated human pluripotent stem cells (hPSCs) to both cardiac progenitor cells (CPCs) and EpiCs, and cocultured EpiCs and CPCs in the presence of A83-01, to inhibit TGFβ signaling and EMT, for two weeks.

overall_design: CPCs were differentiated in the WTC-CAAX-RFP constitutive reporter hiPSC line and EpiCs were differentiated in the WTC-LMNB1-eGFP constitutive reporter hiPSC line. Cells were cocultured for 14 days following the previously described protocol, lifted for flow cytometry with Accutase, and resuspended in PBS (Ca2+/Mg2+ free) supplemented with 0.5% BSA and 5μM DAPI. Dead cells were gated out based on DAPI staining. For single cell sequencing, two samples were prepared of live cells from CMs and EpiCs monocultured or cocultured.

first: Sean

last: Palecek


title: Hydrogen sulfide, a novel small molecule signalling agent, participates in GAs biosynthesis under heat stress and the regulation of multiple signaling pathway genes in Ganoderma lucidum

city: Nanjing

first: jia long

last: tian

address: 1 Weigang

institute: Nanjing Agricultural University

summary: As one of the most important environmental factors, heat stress (HS) has been found to affect various biological activities of organisms such as growth, signal transmission, primary metabolism and secondary metabolism. Ganoderma lucidum has become a potential model system for evaluating how environmental factors regulate the secondary metabolism of basidiomycetes. Previous research showed that HS can induce the biosynthesis of ganoderic acids (GAs). In this study, we found the existence of hydrogen sulfide in Ganoderma lucidum; moreover, HS increased GAs biosynthesis and could affect the hydrogen sulfide content. We found that sodium hydrosulfide (NaHS), an exogenous donor of hydrogen sulfide, could revert the increased GAs biosynthesis elicited by HS. This result indicated that an increased content of hydrogen sulfide, within limits, was associated with HS-induced GAs biosynthesis. Our results further showed that the GAs content was increased in CBS-silenced strains and could be reverted to WT strain levels by the addition of NaHS. Transcriptomic analyses indicated that that H2S can affect various intracellular signal pathways and physiological processes in G. lucidum. Further studies showed that H2S could affect the intracellular calcium concentration and thus regulate the biosynthesis of GAs. This study demonstrated that hydrogen sulfide is involved in the regulation of secondary metabolic processes induced by heat stress in filamentous fungi.

overall_design: G. lucidum mRNA profiles of  wild type (WT) and CBS-silenced strains were generated by deep sequencing, in triplicate

first: Jia

last: Tian

first: Ang

last: Ren